Iodine in PDB 4qu3: Ges-2 Ertapenem Acyl-Enzyme Complex

The structure of Ges-2 Ertapenem Acyl-Enzyme Complex, PDB code: 4qu3 was solved by N.K.Stewart, C.A.Smith, H.Frase, D.J.Black, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.85 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.001, 81.329, 71.895, 90.00, 101.97, 90.00
R / Rfree (%)	15.8 / 19.7

The structure of Ges-2 Ertapenem Acyl-Enzyme Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iodine atom in the Ges-2 Ertapenem Acyl-Enzyme Complex (pdb code 4qu3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Ges-2 Ertapenem Acyl-Enzyme Complex, PDB code: 4qu3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:30.7 occ:0.46 O A:HOH800 3.2 42.9 1.0 NH2 B:ARG105 3.4 13.5 1.0 NE2 A:GLN210 3.4 13.1 1.0 NH1 B:ARG105 3.5 13.1 1.0 CB B:PRO101 3.8 13.8 1.0 CZ B:ARG105 3.9 12.6 1.0 O B:HOH567 4.2 13.9 0.3 CD A:GLN210 4.2 13.7 1.0 O A:HOH827 4.2 42.4 1.0 CG B:PRO101 4.3 12.7 1.0 CD2 B:LEU124 4.3 15.3 1.0 CG A:GLN210 4.4 10.8 1.0 CB A:GLN210 4.4 10.7 1.0 CD1 B:LEU124 4.4 15.1 1.0 O B:HOH567 4.5 13.0 0.7 CH2 B:TRP99 4.5 22.8 1.0 CZ2 B:TRP99 4.7 21.6 1.0 CG B:LEU124 4.9 13.9 1.0 O A:GLN210 5.0 12.8 1.0

Iodine binding site 2 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:38.2 occ:0.42 O B:HOH584 3.2 28.5 1.0 OE1 B:GLN210 3.5 15.6 1.0 NH2 A:ARG105 3.5 18.7 1.0 NH1 A:ARG105 3.5 17.6 1.0 O B:HOH567 3.8 13.9 0.3 CB A:PRO101 3.9 17.1 1.0 CZ A:ARG105 3.9 16.9 1.0 CD2 A:LEU124 4.0 16.3 1.0 CD B:GLN210 4.1 12.8 1.0 CG A:PRO101 4.3 15.9 1.0 CB B:GLN210 4.4 10.8 1.0 CG B:GLN210 4.4 11.4 1.0 CD1 A:LEU124 4.6 15.3 1.0 CH2 A:TRP99 4.8 26.7 1.0 CG A:LEU124 4.9 13.7 1.0

Iodine binding site 3 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:56.5 occ:0.40 CA A:CA502 3.4 13.6 1.0 N A:ASP94 4.1 16.5 1.0 CB A:ASP94 4.2 21.8 1.0 CG A:PRO93 4.2 17.2 1.0 CA A:ASP94 4.4 19.4 1.0 CB A:PRO93 4.7 16.3 1.0 C A:PRO93 4.7 15.1 1.0

Iodine binding site 4 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:56.5 occ:1.00 NH1 A:ARG204 3.3 10.4 1.0 O B:HOH618 3.4 39.2 1.0 O B:HOH606 3.4 40.4 1.0 CD A:ARG204 3.9 11.2 1.0 CD1 A:ILE207 3.9 10.9 1.0 CB B:SER109 4.1 10.5 1.0 CE1 A:HIS200 4.1 23.6 1.0 CE1 B:HIS111 4.4 15.0 1.0 CZ A:ARG204 4.4 9.8 1.0 CD A:GLU203 4.4 30.1 1.0 OE2 A:GLU203 4.4 33.0 1.0 NE A:ARG204 4.6 9.4 1.0 OG B:SER109 4.7 11.4 1.0 OE1 A:GLU203 4.7 33.7 1.0 CG A:GLU203 4.7 22.8 1.0 ND1 A:HIS200 4.8 22.6 1.0

Iodine binding site 5 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:30.1 occ:0.43 NH1 B:ARG204 3.4 11.8 1.0 O A:HOH774 3.4 28.3 1.0 O B:HOH541 3.8 28.8 1.0 CD B:ARG204 3.9 11.4 1.0 CD1 B:ILE207 3.9 10.9 1.0 CB A:SER109 4.1 10.6 1.0 CE1 A:HIS111 4.2 15.1 1.0 OE1 B:GLU203 4.2 27.5 1.0 CE1 B:HIS200 4.3 23.4 1.0 CD B:GLU203 4.4 24.0 1.0 CZ B:ARG204 4.5 10.7 1.0 OE2 B:GLU203 4.6 25.2 1.0 NE B:ARG204 4.7 9.7 1.0 OG A:SER109 4.8 10.7 1.0 ND1 B:HIS200 4.9 22.5 1.0 NE2 A:HIS111 5.0 15.7 1.0 CG B:GLU203 5.0 19.1 1.0

Iodine binding site 6 out of 6 in the Ges-2 Ertapenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Ges-2 Ertapenem Acyl-Enzyme Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:25.6 occ:0.50 O B:HOH421 3.1 21.0 1.0 CA B:GLY139 3.9 16.3 1.0 CD B:PRO140 4.0 13.5 1.0 O B:HOH540 4.0 35.0 1.0 CB B:LEU134 4.1 11.0 1.0 CD B:LYS160 4.2 18.9 1.0 C B:LEU134 4.3 11.1 1.0 N B:ARG135 4.3 11.8 1.0 O B:LEU134 4.3 12.7 1.0 CB B:LYS160 4.5 15.4 1.0 CA B:ARG135 4.5 13.4 1.0 N B:GLY139 4.8 17.7 1.0 CA B:LEU134 4.8 10.9 1.0 O B:HOH514 4.9 28.0 1.0 CG B:LYS160 4.9 16.8 1.0 N B:PRO140 4.9 12.8 1.0 CG B:PRO140 4.9 12.9 1.0 C B:GLY139 4.9 15.2 1.0

N.K.Stewart, C.A.Smith, H.Frase, D.Black, S.B.Vakulenko. Kinetic and Structural Requirements For Carbapenemase Activity in Ges-Type Beta-Lactamases. Biochemistry 2014.
ISSN: ISSN 0006-2960
PubMed: 25485972
DOI: 10.1021/BI501052T